Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0309810939:

Variant ID: vg0309810939 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 9810939
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCGACCTGGAGGCGCAGTTGCACCTTGCGTGCGACGACGGTGAGCCTCGGTCTTTTGCAGAGGCCGAGAAACATGCGGCATGGCGTGCCGCGATGCGG[T/A]
CGGAGATGGACGCGGTTCAGGAGAACCGCACCTGGGAGCTTGCTGACCTCCCTCGTGGTCACCGCGCGATCACCCTTAAGTGGGTGTTCAAGCTGAAGAG

Reverse complement sequence

CTCTTCAGCTTGAACACCCACTTAAGGGTGATCGCGCGGTGACCACGAGGGAGGTCAGCAAGCTCCCAGGTGCGGTTCTCCTGAACCGCGTCCATCTCCG[A/T]
CCGCATCGCGGCACGCCATGCCGCATGTTTCTCGGCCTCTGCAAAAGACCGAGGCTCACCGTCGTCGCACGCAAGGTGCAACTGCGCCTCCAGGTCGCGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.20%	4.80%	0.00%	0.00%	NA
All Indica	2759	99.00%	1.00%	0.00%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	31.60%	68.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0309810939	T -> A	LOC_Os03g17634.1	intron_variant ; MODIFIER	silent_mutation	Average:47.908; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0309810939	4.51E-06	NA	mr1219	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0309810939	NA	6.52E-06	mr1259	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0309810939	7.55E-06	4.38E-06	mr1219_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251